If you use QuickBooks Online to manage transactions from PayPal, you might have recently seen an alert about the Connect to PayPal app being retired.
This change has left many business owners wondering what to do next, how to update their PayPal connection, and whether the new replacement is actually a good option.
In this guide, we’ll explain what’s happening with the Connect to PayPal app, what your options are, and how to update your PayPal integration in QuickBooks Online without disrupting your bookkeeping.
What’s Happening to the Connect to PayPal App?
At the end of March 2025, Intuit is retiring the Connect to PayPal app in QuickBooks Online. If you previously used this integration to sync PayPal transactions automatically, you’ll need to update your settings to avoid losing access to PayPal feeds.
What Does This Mean for You?
- If you use the Connect to PayPal app, you will see a notification in QuickBooks telling you that the connection is ending.
- If you don’t update your connection, PayPal transactions will stop syncing.
- Intuit is pushing users toward the new PayPal Connector app—but it’s not the same as the old integration, and it comes with limitations.
🚨 Shopify Problem: If you use Shopify with PayPal, the new PayPal Connector won’t import transactions that originate from Shopify. This means business owners who rely on Shopify payments processed through PayPal will have gaps in their bookkeeping.
If you’re unsure how this affects your business, it’s a good idea to test the new connection before fully switching over.
How I Updated My PayPal Connection in QuickBooks Online
My QuickBooks was connected to the Connect to PayPal app. Which is how I knew this problem existed (I got the warning).
I don’t need sales receipts so I disconnected and reconnected using the PayPal integration that’s still available.
🚨 Important: Before disconnecting, make sure all pending PayPal transactions are categorized to prevent duplicates later.
Step 1: Disconnect Connect to PayPal
- Navigate to Bank Transactions.
- Find your PayPal account card and click the pencil icon in the upper right corner.
- Click Edit settings.
- Click Disconnect PayPal.
- Enter a reason for disconnecting and click Submit.
Step 2: Reconnect Using the PayPal.com Integration
Once you’ve disconnected Connect to PayPal, you can reconnect using the one simply labeled PayPal that’s still available.
- Click Link Account.
- Search for “PayPal”.
- Choose the PayPal connection (NOT “Connect to PayPal”).
- Follow the prompts to log into your PayPal account and grant QuickBooks permission.
- Select the account in QuickBooks that will be linked to your PayPal account.
- Set the sync start date—it’s best to choose Today to avoid pulling in duplicate transactions.
- Click Connect, then Done.
💡 Pro Tip: If you have a large volume of PayPal transactions, you might notice a few missing transactions when reconciling. If this happens, manually enter any missing transactions instead of re-importing everything.
Want to see these steps in action? Watch the video below:
Should You Use the New PayPal Connector App?
Intuit is encouraging users to switch to the new PayPal Connector app, but it doesn’t work the same way as the old Connect to PayPal integration.
This is an actual app that you’ll need to connect through the Apps section. You will NOT find it if you click Link Account in Bank Transactions.
Pros of the New PayPal Connector App:
- Syncs PayPal transactions automatically
- Allows income to be categorized directly
- Still supported by Intuit (unlike Connect to PayPal)
Cons of the New PayPal Connector App:
- Does NOT sync Shopify transactions processed through PayPal
- Still has occasional duplicate transaction issues
- Requires extra setup and review to ensure accuracy
Who Should Consider Alternative Solutions?
If you need detailed tracking of PayPal transactions, or if you sell on Shopify and use PayPal, the new PayPal Connector may not be your best option.
Instead, look into third-party PayPal-to-QuickBooks integrations like:
- A2X (great for high-volume sellers)
- Bookkeep.com (automates reconciliation for multiple platforms)
- SaasAnt (for bulk importing transactions)
These tools help ensure you don’t lose any sales data or double-enter transactions when using Shopify or other e-commerce platforms.
How to Troubleshoot Common Issues After Updating Your PayPal Connection
After switching from Connect to PayPal to the newer integration, you may run into a few common issues. Here’s how to fix them:
Problem 1: Missing Transactions
- Check your PayPal balance and match it to what’s in QuickBooks.
- If transactions are missing, manually enter them or use a third-party importer like SaasAnt.
Problem 2: Duplicate Transactions
- If you see duplicates, check if the PayPal transactions are also pulling from your bank feed.
- Manually exclude duplicate entries to avoid overinflating income.
Final Thoughts: Navigating the Connect to PayPal App Retirement
If you’ve been using Connect to PayPal in QuickBooks Online, now is the time to update your connection to avoid disruptions. While Intuit is pushing the new PayPal Connector app, it may not work for every business—especially Shopify users.
Key Takeaways:
- The Connect to PayPal app is being retired at the end of March 2025.
- You must disconnect and reconnect PayPal in QuickBooks Online to continue syncing transactions.
- Shopify transactions processed through PayPal will NOT sync in the new PayPal Connector app.
- Third-party apps like A2X, Bookkeep.com, and SaasAnt can help e-commerce businesses fill the gaps.
- Always review your transactions after updating your PayPal connection to avoid duplicates or missing entries.
If you need help fixing your PayPal connection in QuickBooks, I offer one-on-one QuickBooks coaching to walk you through the process and ensure everything is set up correctly.
📌 Book a session at GentleFrog.com/meeting
